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Description

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Quick Start

This template includes a tutorial workflow that demonstrates Nextflow 25.10 best practices (according to me).

Tutorial Example: Greeting Document Generator

The tutorial workflow generates personalized greeting documents from a samplesheet:

# Run the tutorial workflow
NXF_VER=25.10.0 nextflow run . \
    --input tests/data/samplesheet.csv \
    --output_format pdf

# Try different output formats
NXF_VER=25.10.0 nextflow run . \
    --input tests/data/samplesheet.csv \
    --output_format rtf

What it demonstrates:

• ✅ Typed params block (NF 25.10+)
• ✅ Parameters passed via meta, not used directly in processes
• ✅ Workflow outputs with publish: and output {} blocks
• ✅ Workflow handlers (onComplete, onError)
• ✅ Dynamic values passed through metadata
• ✅ nf-test for testing

Samplesheet format (tests/data/samplesheet.csv):

sample,title,level
Alice,Ms,intermediate
Bob,Mr,beginner
Charlie,Dr,advanced

Testing

This template uses nf-test for testing.

# Install nf-test (if not already installed)
curl -fsSL https://get.nf-test.com | bash

# Run specific test
nf-test test main.nf.test

# Run with verbose output
nf-test test --verbose

Documentation convention

• RESOURCES.md - Resource configuration and dynamic resources
• CONTRIBUTE.md - General contribution guidelines
• modules/process/README.md - Process development guidelines (NF 25.10+)
• CHANGELOG.md - Version history and migration notes